The efficiency of eco-environmental governance can be influenced by a variety of factors, and different factors have different effects on eco-environmental governance efficiency. This study attempts to investigate the impact of environmental protection input on the efficiency of ecological environmental governance in China. By using Meta-analysis, the effects of environmental protection input on eco-environmental governance efficiency were selected under 35 independent samples studying eco-environmental governance efficiency in China from 2010 to 2022. Meta-binary analysis and regression analysis were also used to explore the moderating effects of potential moderating variables on the relationship between environmental protection input and eco-environmental governance efficiency. The empirical results demonstrate that: (1) environmental protection inputs have a significant positive effect on the efficiency of eco-environmental governance in China in all dimensions. (2) The relationship between environmental protection input and eco-environmental governance efficiency is moderated by measurement scope, measurement dimension, technological innovation, and environmental regulation. Based on the empirical findings, this study further proposes policy recommendations to improve the efficiency of China’s eco-environmental governance, including increasing environmental protection investment, playing a leading role in the government, addressing regional economic differences, increasing scientific and technological innovation, and improving the environmental regulation system.